I.1. Modern humans

Initial Upper Palaeolithic industries associated with the spread of anatomically modern humans could have begun as early as 48000 BC, with Emirian lithics found in the Negev Desert ca. 45000–43000 BC. This first expansion was followed by another successful one from the Levant, represented by the Early Ahmarian (Near East), Kozarnikian (eastern Balkans), and Proto-Aurignacian (south-west and south-central European) lithic cultures.

Admixture with Neanderthals probably took place in the levant during these early population movements out of Africa, as seen in an Upper Palaeolithic Siberian—Ust’Ishim ca. 43000 BC (Fu et al. 2014), of hg. K-M9(xLT)—and an early Upper Palaeolithic East Asian population—Tianyuan ca. 40500 BC (Yang et al. 2017). The so-called Basal Eurasians, not yet sampled, do not show this admixture, which indicates that they formed part of another expanding group, probably located somewhere in the Near East.

By ca. 39000 BC, modern humans had spread into southern Europe, with transitional industries from Middle Palaeolithic Mousterian style (typical of Neanderthals) to Upper Palaeolithic cultures found widespread in Europe: Uluzzian in northern and southern Italy and Greece; Châtelperronian in northern Spain and western and central France; Szeletian in the Czech Republic and Hungary; and the Lincombian–Ranisian–Jerzmanowician from east to west across the Northern European plain.

These pioneer populations in Europe, represented by Ust’Ishim in Siberia and by the Oase1 individual from Romania ca. 38000 BC, who shows a recent Neanderthal contribution less than six generations back in his family tree, did not contribute detectably to any present-day European population, which suggests that later population expansions have wiped out most of their genetic contribution. It has been speculatively proposed that these populations were affected by the eruption of the Archiflegreo volcano ca. 37000 BC, like Neanderthals, and were thus more easily replaced by newcomers.

Populations that began to diverge 40,000 years ago or earlier in Eurasia may thus be simplistically divided into geographic regions—without care for sub-structured populations and gene flow—as (Suppl. Fig. 1):

· Ancestral North Africans (ANA): a deeply splitting ghost population without Neanderthal admixture, assumed to be present during the Upper Palaeolithic in northern Africa.

· Basal Eurasians (BE): another “deep” ghost population, not participating in the Neanderthal admixture, assumed to have diverged from other non-African Eurasian populations ca. 67,400–101,000 years ago. It experienced most of the common bottleneck of non-Basal Eurasians, which suggests their common involvement in their further migration to the Levant (Lazaridis et al. 2018).

· Upper Palaeolithic Siberians: represented by Ust’Ishim and Oase1, they stem from a common Main Eurasian population which admixed with Neanderthals.

· Early East Asians (EEA): represented by Tianyuan[4], mainly contributed to by a common source to Upper Palaeolithic Siberians (ca. 98%). It also represents the ancestral population of eastern non-Africans (ENA) —i.e. modern Papuans and Onge, and a contribution of some Native Americans—which in turn contributes to present-day South and East Asians.

· Early West Eurasians (EWE): with the earliest representative samples being far eastern Europeans Kostenki14 and Sunghir3, their parent population—probably widespread through Eastern Europe, the Caucasus and the Near East—contributed for thousands of years to different Upper Palaeolithic and Mesolithic migrations, and their ancestry is found in present-day Europeans and Near Easterners.